diff --git a/.ebextensions/02_download_variant_data_commands.config b/.ebextensions/02_app_config.config similarity index 80% rename from .ebextensions/02_download_variant_data_commands.config rename to .ebextensions/02_app_config.config index a3c31431..a4f15662 100644 --- a/.ebextensions/02_download_variant_data_commands.config +++ b/.ebextensions/02_app_config.config @@ -1,50 +1,50 @@ -container_commands: - 01_export_eb_env_var: - command: "export $(cat /opt/elasticbeanstalk/deployment/env | xargs)" - - 02_install_awscli: +commands: + 01_install_postgresql_devel: + command: "yum install -y python-devel postgresql-devel" + 02_install_aws_cli: command: "yum install -y awscli" - 03_install_unzip: - test: test ! -d "/usr/local/share/seqrepo" command: "yum install -y unzip" + 04_export_eb_env_var: + command: "export $(cat /opt/elasticbeanstalk/deployment/env | xargs)" - 05_refseq_gene_symbols_download: +container_commands: + 01_refseq_gene_symbols_download: test: test ! -f "/var/app/venv/staging-LQM1lest/lib/python3.8/site-packages/variation/data/refseq_gene_symbols.txt" command: "aws s3 cp s3://${AWS_BUCKET_NAME}/variation/refseq_gene_symbols.txt /var/app/venv/staging-LQM1lest/lib/python3.8/site-packages/variation/data/refseq_gene_symbols.txt --region us-east-2" - 06_mane_grch38_refseq_download: + 02_mane_grch38_refseq_download: test: test ! -f "/var/app/venv/staging-LQM1lest/lib/python3.8/site-packages/variation/data/MANE.GRCh38.v0.93.summary.txt" command: "aws s3 cp s3://${AWS_BUCKET_NAME}/variation/MANE.GRCh38.v0.93.summary.txt /var/app/venv/staging-LQM1lest/lib/python3.8/site-packages/variation/data/MANE.GRCh38.v0.93.summary.txt --region us-east-2" - 07_s3_download: + 03_s3_download: test: test ! -d "/usr/local/share/seqrepo" command: "aws s3 cp s3://${AWS_BUCKET_NAME}/${AWS_SEQREPO_OBJECT} /usr/local/share/seqrepo.zip --region us-east-2" - 08_unzip_seqrepo: + 04_unzip_seqrepo: test: test -f "/usr/local/share/seqrepo.zip" command: "unzip /usr/local/share/seqrepo.zip -d /usr/local/share" - 09_seqrepo_permission: + 05_seqrepo_permission: test: test -d "/usr/local/share/seqrepo" command: "chmod -R 777 /usr/local/share/seqrepo" - 10_macosx_permission: + 06_macosx_permission: test: test -d "/usr/local/share/__MACOSX" command: "chmod -R +wr /usr/local/share/__MACOSX" - 11_seqrepo_zip_permission: + 07_seqrepo_zip_permission: test: test -f "/usr/local/share/seqrepo.zip" command: "chmod +wr /usr/local/share/seqrepo.zip" - 12_remove_macosx: + 08_remove_macosx: test: test -d "/usr/local/share/__MACOSX" command: "rm -R /usr/local/share/__MACOSX" - 13_remove_seqrepo_zip: + 09_remove_seqrepo_zip: test: test -f "/usr/local/share/seqrepo.zip" command: "rm /usr/local/share/seqrepo.zip" - 14_data_permission: + 10_data_permission: test: test -d "/usr/local/share/seqrepo" command: "chmod -R +wrx /usr/local/share/seqrepo"